Convert PETRA head images to density maps. Work in progress, things may change.
- Linux
- Python
- Simnibs
See the simnibs docs for installation instructions.
Activate the simnibs conda environment.
python petra2density.py SUBJECT_ID /path/to/T1.nii.gz /path/to/PETRA.nii.gz /path/to/output_folder [--register_to_petra] [--ct2density_calibration_file /path/to/calibration_file.csv] [--kplan]
Output_folder should already exist. Creates output_folder/SUBJECT_ID/m2m_SUBJECT_ID.
The density image is here: output_folder/SUBJECT_ID/m2m_SUBJECT_IDdensity.nii.gz.
Use --register_to_petra to register to the PETRA image. Default is to register to the T1 image.
Use --kplan to align the image to a space compatible with kplan.
Based on work from petra-to-ct.